HI all,can someone please tell me if there is any dye, either fluorescent or non-fluorescent, which can bind differentially to supercoiled and relaxed plasmid so that i should be able to measure the difference in the supercoiling of the plasmid just by taking absorbance instead of time consuming gel running.If i can do it in a 96 well plate then it's fantasticthanking you in advanceLeelaram

-leelaram-

I don't think so. I don't think supercoiling changes the structure of the grooves in DNA, to which ethidium bromide and the like bind. It is more of a gross packaging of the DNA. Running a gel isn't that time consuming is it?

-killerkoz17-

Hi Killerkoz,I accept with you but depending on the concentration of the dye there will be a change in the supercoiling of DNA and hence the amount of dye bound so that the fluorescence intensity differsawaiting your suggestionsLeelaram

-leelaram-

QUOTE (leelaram @ Nov 18 2007, 02:28 AM)

Hi Killerkoz,I accept with you but depending on the concentration of the dye there will be a change in the supercoiling of DNA and hence the amount of dye bound so that the fluorescence intensity differsawaiting your suggestionsLeelaram

Didn't know that, I'm no help then!

-killerkoz17-

Hi Killerkoz,i got the answer and thought i would let you know the informationDNA intercalating agents like EtBr can bind differentially to supercoiled and relaxed DNAanother agent Psoralen also binds efficiently to supercoiled DNA but not so much to relaxed DNA. if the psoralen is biotinylated then supercoiled DNA can be detected by streptavidin conjugated ALP or HRP and then with a chromogenic substratehope I am clearLeelaram

-leelaram-

QUOTE (leelaram @ Nov 18 2007, 10:30 PM)

Hi Killerkoz,i got the answer and thought i would let you know the informationDNA intercalating agents like EtBr can bind differentially to supercoiled and relaxed DNAanother agent Psoralen also binds efficiently to supercoiled DNA but not so much to relaxed DNA. if the psoralen is biotinylated then supercoiled DNA can be detected by streptavidin conjugated ALP or HRP and then with a chromogenic substratehope I am clearLeelaram